Load R libraries

library(Amelia)
## Loading required package: Rcpp
## ## 
## ## Amelia II: Multiple Imputation
## ## (Version 1.7.4, built: 2015-12-05)
## ## Copyright (C) 2005-2018 James Honaker, Gary King and Matthew Blackwell
## ## Refer to http://gking.harvard.edu/amelia/ for more information
## ##
library(mice)
## Loading required package: lattice
library(miceadds)
## * miceadds 2.9-15 (2017-12-18 11:50:04)
library(ggplot2)
library(lattice)

Load vehicle data without missing target.

setwd("/Users/davidleonardi/Projects/KE5107_BayesianNetworks/")
data <- read.csv("./vehicle_safety_remove_missing_target.csv")
data$GV_LANES <- as.factor(data$GV_LANES)
data$GV_MODELYR <- as.factor(data$GV_MODELYR)
data$GV_WGTCDTR <- as.factor(data$GV_WGTCDTR)
data$OA_BAGDEPLY <- as.factor(data$OA_BAGDEPLY)
data$OA_MAIS <- as.factor(data$OA_MAIS)
data$OA_MANUSE <- as.factor(data$OA_MANUSE)
data$OA_SEX <- as.factor(data$OA_SEX)
data$VE_GAD1 <- as.factor(data$VE_GAD1)

summary(data)
##    GV_CURBWGT      GV_DVLAT          GV_DVLONG         GV_ENERGY     
##  Min.   : 670   Min.   :-114.000   Min.   :-145.00   Min.   :   4.0  
##  1st Qu.:1360   1st Qu.:  -6.000   1st Qu.: -23.00   1st Qu.: 155.0  
##  Median :1530   Median :   0.000   Median : -15.00   Median : 305.0  
##  Mean   :1618   Mean   :   0.113   Mean   : -14.75   Mean   : 501.5  
##  3rd Qu.:1830   3rd Qu.:   7.000   3rd Qu.:  -8.00   3rd Qu.: 598.0  
##  Max.   :4310   Max.   : 118.000   Max.   :  84.00   Max.   :9852.0  
##  NA's   :39     NA's   :5877       NA's   :5877      NA's   :5877    
##     GV_LANES      GV_MODELYR    GV_OTVEHWGT     GV_SPLIMIT   
##  2      :7347   2000   :2670   Min.   : 640   Min.   : 0.00  
##  4      :3922   2002   :2659   1st Qu.:1340   1st Qu.:35.00  
##  3      :3520   2001   :2577   Median :1550   Median :40.00  
##  5      :2981   2003   :2348   Mean   :1630   Mean   :40.72  
##  6      : 651   2004   :2048   3rd Qu.:1840   3rd Qu.:45.00  
##  (Other): 779   2005   :1896   Max.   :4540   Max.   :75.00  
##  NA's   :   3   (Other):5005   NA's   :1992   NA's   :221    
##                 GV_WGTCDTR        OA_AGE            OA_BAGDEPLY   
##  Passenger Car       :11800   Min.   : 0.00   Deployed    : 9017  
##  Truck (<=10000 lbs.): 2414   1st Qu.:25.00   Not Deployed:10186  
##  Truck (<=6000 lbs.) : 4989   Median :37.00                       
##                               Mean   :40.23                       
##                               3rd Qu.:52.00                       
##                               Max.   :97.00                       
##                               NA's   :14                          
##    OA_HEIGHT     OA_MAIS  OA_MANUSE       OA_SEX       OA_WEIGHT    
##  Min.   : 59.0   0:7319   0   : 2175         : 201   Min.   : 31.0  
##  1st Qu.:163.0   1:8814   1   :16643   Female:9453   1st Qu.: 64.0  
##  Median :170.0   2:1517   NA's:  385   Male  :9549   Median : 77.0  
##  Mean   :170.8   3: 950                              Mean   : 78.8  
##  3rd Qu.:178.0   4: 301                              3rd Qu.: 91.0  
##  Max.   :216.0   5: 217                              Max.   :150.0  
##  NA's   :2116    6:  85                              NA's   :2008   
##   VE_GAD1       VE_ORIGAVTW     VE_WHEELBAS      VE_PDOF_TR   
##       :  771   Min.   :105.0   Min.   :141.0   Min.   :  5.0  
##  Front:11176   1st Qu.:149.0   1st Qu.:262.0   1st Qu.:115.0  
##  Left : 2997   Median :154.0   Median :272.0   Median :135.0  
##  Rear : 1629   Mean   :154.8   Mean   :281.1   Mean   :152.2  
##  Right: 2630   3rd Qu.:158.0   3rd Qu.:288.0   3rd Qu.:175.0  
##                Max.   :185.0   Max.   :481.0   Max.   :355.0  
##                NA's   :219     NA's   :8       NA's   :1864   
##   GV_FOOTPRINT  
##  Min.   :2.468  
##  1st Qu.:3.925  
##  Median :4.200  
##  Mean   :4.364  
##  3rd Qu.:4.554  
##  Max.   :7.795  
##  NA's   :223

Show missing data in diagram.

missmap(data[-1], col=c('grey', 'steelblue'), y.cex=0.5, x.cex=0.8)

Get hard numbers of missing data.

# Let's also get some hard numbers
sort(sapply(data, function(x) { sum(is.na(x)) }), decreasing=TRUE)
##     GV_DVLAT    GV_DVLONG    GV_ENERGY    OA_HEIGHT    OA_WEIGHT 
##         5877         5877         5877         2116         2008 
##  GV_OTVEHWGT   VE_PDOF_TR    OA_MANUSE GV_FOOTPRINT   GV_SPLIMIT 
##         1992         1864          385          223          221 
##  VE_ORIGAVTW   GV_CURBWGT       OA_AGE  VE_WHEELBAS     GV_LANES 
##          219           39           14            8            3 
##   GV_MODELYR   GV_WGTCDTR  OA_BAGDEPLY      OA_MAIS       OA_SEX 
##            0            0            0            0            0 
##      VE_GAD1 
##            0

Show missing data pattern.

md.pattern(data)
##       GV_MODELYR GV_WGTCDTR OA_BAGDEPLY OA_MAIS OA_SEX VE_GAD1 GV_LANES
## 10930          1          1           1       1      1       1        1
##     5          1          1           1       1      1       1        1
##     2          1          1           1       1      1       1        0
##   250          1          1           1       1      1       1        1
##    97          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##   138          1          1           1       1      1       1        1
##    51          1          1           1       1      1       1        1
##    64          1          1           1       1      1       1        1
##   385          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     4          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     2          1          1           1       1      1       1        1
##     4          1          1           1       1      1       1        1
##     2          1          1           1       1      1       1        1
##  1122          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     7          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     5          1          1           1       1      1       1        1
##     7          1          1           1       1      1       1        1
##    77          1          1           1       1      1       1        1
##  2436          1          1           1       1      1       1        1
##    25          1          1           1       1      1       1        1
##    20          1          1           1       1      1       1        1
##     5          1          1           1       1      1       1        1
##    48          1          1           1       1      1       1        1
##    24          1          1           1       1      1       1        1
##     4          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     3          1          1           1       1      1       1        1
##     2          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     8          1          1           1       1      1       1        1
##    15          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        0
##  1221          1          1           1       1      1       1        1
##    35          1          1           1       1      1       1        1
##    30          1          1           1       1      1       1        1
##    69          1          1           1       1      1       1        1
##    13          1          1           1       1      1       1        1
##     2          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##   969          1          1           1       1      1       1        1
##     4          1          1           1       1      1       1        1
##    15          1          1           1       1      1       1        1
##     3          1          1           1       1      1       1        1
##     2          1          1           1       1      1       1        1
##     8          1          1           1       1      1       1        1
##    16          1          1           1       1      1       1        1
##    22          1          1           1       1      1       1        1
##     3          1          1           1       1      1       1        1
##     7          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     8          1          1           1       1      1       1        1
##   249          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     4          1          1           1       1      1       1        1
##   210          1          1           1       1      1       1        1
##    25          1          1           1       1      1       1        1
##     4          1          1           1       1      1       1        1
##    24          1          1           1       1      1       1        1
##     6          1          1           1       1      1       1        1
##    41          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     2          1          1           1       1      1       1        1
##     2          1          1           1       1      1       1        1
##     2          1          1           1       1      1       1        1
##   152          1          1           1       1      1       1        1
##     2          1          1           1       1      1       1        1
##     3          1          1           1       1      1       1        1
##    68          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     2          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     3          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     2          1          1           1       1      1       1        1
##    80          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##    12          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     3          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##    20          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##    12          1          1           1       1      1       1        1
##     4          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##    16          1          1           1       1      1       1        1
##     2          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##    25          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     3          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     8          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     4          1          1           1       1      1       1        1
##     3          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     2          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     1          1          1           1       1      1       1        1
##     2          1          1           1       1      1       1        1
##                0          0           0       0      0       0        3
##       VE_WHEELBAS OA_AGE GV_CURBWGT VE_ORIGAVTW GV_SPLIMIT GV_FOOTPRINT
## 10930           1      1          1           1          1            1
##     5           1      1          0           1          1            1
##     2           1      1          1           1          1            1
##   250           1      1          1           1          1            1
##    97           1      1          1           1          0            1
##     1           1      0          1           1          1            1
##   138           1      1          1           1          1            1
##    51           1      1          1           1          1            1
##    64           1      1          1           1          1            1
##   385           1      1          1           1          1            1
##     1           1      1          1           1          0            1
##     1           1      0          1           1          1            1
##     4           1      1          1           1          1            1
##     1           1      1          1           1          0            1
##     2           1      1          1           1          1            1
##     4           1      1          1           1          1            1
##     2           1      1          1           1          0            1
##  1122           1      1          1           1          1            1
##     1           1      1          1           1          1            1
##     1           1      1          1           1          1            1
##     7           1      1          1           1          0            1
##     1           1      1          1           1          1            1
##     5           1      1          1           1          1            1
##     7           1      1          1           1          1            1
##    77           1      1          1           0          1            0
##  2436           1      1          1           1          1            1
##    25           1      1          1           1          1            1
##    20           1      1          1           1          0            1
##     5           1      0          1           1          1            1
##    48           1      1          1           1          1            1
##    24           1      1          1           1          1            1
##     4           1      1          1           0          1            0
##     1           1      1          1           0          0            0
##     3           1      1          1           0          1            0
##     2           1      1          1           0          1            0
##     1           0      1          0           1          1            0
##     8           1      1          1           0          1            0
##    15           1      1          0           1          1            1
##     1           1      1          1           1          1            1
##  1221           1      1          1           1          1            1
##    35           1      1          1           1          0            1
##    30           1      1          1           1          1            1
##    69           1      1          1           1          1            1
##    13           1      1          1           1          1            1
##     2           1      1          1           1          0            1
##     1           1      0          1           1          1            1
##   969           1      1          1           1          1            1
##     4           1      1          1           1          1            1
##    15           1      1          1           0          1            0
##     3           1      1          0           1          1            1
##     2           1      1          0           1          0            1
##     8           1      1          1           1          0            1
##    16           1      1          1           1          1            1
##    22           1      1          1           1          1            1
##     3           1      1          1           1          0            1
##     7           1      1          1           1          1            1
##     1           1      1          0           1          1            1
##     8           1      1          1           1          1            1
##   249           1      1          1           1          1            1
##     1           1      1          1           1          1            1
##     4           1      1          0           1          1            1
##   210           1      1          1           1          1            1
##    25           1      1          1           1          0            1
##     4           1      1          1           1          1            1
##    24           1      1          1           1          1            1
##     6           1      1          1           1          1            1
##    41           1      1          1           0          1            0
##     1           1      0          1           0          1            0
##     2           1      1          1           0          1            0
##     2           0      1          1           1          1            0
##     2           1      1          0           1          1            1
##   152           1      1          1           1          1            1
##     2           1      1          1           1          0            1
##     3           1      0          1           1          1            1
##    68           1      1          1           1          1            1
##     1           1      1          0           1          1            1
##     2           1      1          1           1          0            1
##     1           1      1          1           1          1            1
##     3           1      1          1           1          1            1
##     1           1      1          1           1          0            1
##     2           1      1          1           1          1            1
##    80           1      1          1           1          1            1
##     1           1      1          1           1          1            1
##    12           1      1          1           0          1            0
##     1           1      1          1           0          0            0
##     3           1      1          1           0          1            0
##     1           0      1          0           1          1            0
##     1           0      1          1           0          1            0
##    20           1      1          1           0          1            0
##     1           1      1          1           0          1            0
##     1           1      1          0           1          1            1
##    12           1      1          1           1          1            1
##     4           1      1          1           1          0            1
##     1           1      0          1           1          1            1
##     1           1      1          1           1          0            1
##     1           1      1          0           1          1            1
##    16           1      1          1           1          1            1
##     2           1      1          1           1          0            1
##     1           1      0          1           1          1            1
##    25           1      1          1           1          1            1
##     1           1      1          1           0          0            0
##     3           1      1          1           0          1            0
##     1           0      1          0           0          1            0
##     1           0      1          1           0          1            0
##     8           1      1          1           0          1            0
##     1           1      1          1           0          0            0
##     4           1      1          1           0          1            0
##     3           1      1          1           1          1            1
##     1           1      1          1           1          0            1
##     2           1      1          1           0          1            0
##     1           1      1          0           0          1            0
##     1           1      1          1           0          1            0
##     1           1      1          1           1          0            1
##     1           1      1          1           0          1            0
##     1           0      1          1           0          1            0
##     2           1      1          1           0          1            0
##                 8     14         39         219        221          223
##       OA_MANUSE VE_PDOF_TR GV_OTVEHWGT OA_WEIGHT OA_HEIGHT GV_DVLAT
## 10930         1          1           1         1         1        1
##     5         1          1           1         1         1        1
##     2         1          1           1         1         1        1
##   250         1          1           0         1         1        1
##    97         1          1           1         1         1        1
##     1         1          1           1         1         1        1
##   138         1          1           1         1         0        1
##    51         0          1           1         1         1        1
##    64         1          1           1         0         1        1
##   385         1          0           1         1         1        1
##     1         1          1           0         1         1        1
##     1         1          1           0         1         1        1
##     4         1          1           0         1         0        1
##     1         1          1           1         1         0        1
##     2         0          1           0         1         1        1
##     4         0          1           1         1         0        1
##     2         1          1           1         0         1        1
##  1122         1          1           1         0         0        1
##     1         0          1           1         0         1        1
##     1         1          0           0         1         1        1
##     7         1          0           1         1         1        1
##     1         1          0           1         1         0        1
##     5         0          0           1         1         1        1
##     7         1          0           1         0         1        1
##    77         1          1           1         1         1        1
##  2436         1          1           1         1         1        0
##    25         1          1           0         0         0        1
##    20         1          1           1         0         0        1
##     5         1          1           1         0         0        1
##    48         0          1           1         0         0        1
##    24         1          0           1         0         0        1
##     4         1          1           0         1         1        1
##     1         1          1           1         1         1        1
##     3         1          1           1         1         0        1
##     2         0          1           1         1         1        1
##     1         1          1           1         1         1        1
##     8         1          0           1         1         1        1
##    15         1          1           1         1         1        0
##     1         1          1           1         1         1        0
##  1221         1          1           0         1         1        0
##    35         1          1           1         1         1        0
##    30         1          1           1         1         0        0
##    69         0          1           1         1         1        0
##    13         1          1           1         0         1        0
##     2         0          1           1         0         0        1
##     1         0          1           1         0         0        1
##   969         1          0           1         1         1        0
##     4         0          0           1         0         0        1
##    15         1          1           1         0         0        1
##     3         1          1           0         1         1        0
##     2         1          1           1         1         1        0
##     8         1          1           0         1         1        0
##    16         1          1           0         1         0        0
##    22         0          1           0         1         1        0
##     3         0          1           1         1         1        0
##     7         0          1           1         1         0        0
##     1         1          1           1         0         1        0
##     8         1          1           0         0         1        0
##   249         1          1           1         0         0        0
##     1         0          1           1         0         1        0
##     4         1          0           1         1         1        0
##   210         1          0           0         1         1        0
##    25         1          0           1         1         1        0
##     4         1          0           1         1         0        0
##    24         0          0           1         1         1        0
##     6         1          0           1         0         1        0
##    41         1          1           1         1         1        0
##     1         1          1           1         0         0        1
##     2         0          1           1         0         0        1
##     2         1          1           1         1         1        0
##     2         1          1           1         0         0        0
##   152         1          1           0         0         0        0
##     2         1          1           1         0         0        0
##     3         1          1           1         0         0        0
##    68         0          1           1         0         0        0
##     1         1          0           0         1         1        0
##     2         1          0           0         1         1        0
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##     3         0          0           0         1         1        0
##     1         0          0           1         1         1        0
##     2         0          0           1         1         0        0
##    80         1          0           1         0         0        0
##     1         0          0           1         0         1        0
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##     1         1          1           1         1         1        0
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##     1         1          1           1         1         1        0
##     1         1          1           1         1         1        0
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##     1         0          0           1         0         0        1
##     1         0          1           1         0         0        0
##    12         0          1           0         0         0        0
##     4         0          1           1         0         0        0
##     1         0          1           1         0         0        0
##     1         0          0           1         1         0        0
##     1         1          0           1         0         0        0
##    16         1          0           0         0         0        0
##     2         1          0           1         0         0        0
##     1         1          0           1         0         0        0
##    25         0          0           1         0         0        0
##     1         1          1           0         1         1        0
##     3         1          1           1         0         0        0
##     1         1          1           1         1         1        0
##     1         0          1           1         1         1        0
##     8         1          0           0         1         1        0
##     1         1          0           1         1         1        0
##     4         0          0           1         1         1        0
##     3         0          0           0         0         0        0
##     1         0          0           1         0         0        0
##     2         1          1           0         0         0        0
##     1         1          0           0         1         1        0
##     1         1          0           1         0         0        0
##     1         0          0           0         0         0        0
##     1         0          1           0         0         0        0
##     1         0          1           1         0         0        0
##     2         0          0           1         0         0        0
##             385       1864        1992      2008      2116     5877
##       GV_DVLONG GV_ENERGY      
## 10930         1         1     0
##     5         1         1     1
##     2         1         1     1
##   250         1         1     1
##    97         1         1     1
##     1         1         1     1
##   138         1         1     1
##    51         1         1     1
##    64         1         1     1
##   385         1         1     1
##     1         1         1     2
##     1         1         1     2
##     4         1         1     2
##     1         1         1     2
##     2         1         1     2
##     4         1         1     2
##     2         1         1     2
##  1122         1         1     2
##     1         1         1     2
##     1         1         1     2
##     7         1         1     2
##     1         1         1     2
##     5         1         1     2
##     7         1         1     2
##    77         1         1     2
##  2436         0         0     3
##    25         1         1     3
##    20         1         1     3
##     5         1         1     3
##    48         1         1     3
##    24         1         1     3
##     4         1         1     3
##     1         1         1     3
##     3         1         1     3
##     2         1         1     3
##     1         1         1     3
##     8         1         1     3
##    15         0         0     4
##     1         0         0     4
##  1221         0         0     4
##    35         0         0     4
##    30         0         0     4
##    69         0         0     4
##    13         0         0     4
##     2         1         1     4
##     1         1         1     4
##   969         0         0     4
##     4         1         1     4
##    15         1         1     4
##     3         0         0     5
##     2         0         0     5
##     8         0         0     5
##    16         0         0     5
##    22         0         0     5
##     3         0         0     5
##     7         0         0     5
##     1         0         0     5
##     8         0         0     5
##   249         0         0     5
##     1         0         0     5
##     4         0         0     5
##   210         0         0     5
##    25         0         0     5
##     4         0         0     5
##    24         0         0     5
##     6         0         0     5
##    41         0         0     5
##     1         1         1     5
##     2         1         1     5
##     2         0         0     5
##     2         0         0     6
##   152         0         0     6
##     2         0         0     6
##     3         0         0     6
##    68         0         0     6
##     1         0         0     6
##     2         0         0     6
##     1         0         0     6
##     3         0         0     6
##     1         0         0     6
##     2         0         0     6
##    80         0         0     6
##     1         0         0     6
##    12         0         0     6
##     1         0         0     6
##     3         0         0     6
##     1         0         0     6
##     1         0         0     6
##    20         0         0     6
##     1         1         1     6
##     1         0         0     7
##    12         0         0     7
##     4         0         0     7
##     1         0         0     7
##     1         0         0     7
##     1         0         0     7
##    16         0         0     7
##     2         0         0     7
##     1         0         0     7
##    25         0         0     7
##     1         0         0     7
##     3         0         0     7
##     1         0         0     7
##     1         0         0     7
##     8         0         0     7
##     1         0         0     7
##     4         0         0     7
##     3         0         0     8
##     1         0         0     8
##     2         0         0     8
##     1         0         0     8
##     1         0         0     8
##     1         0         0     9
##     1         0         0     9
##     1         0         0     9
##     2         0         0     9
##            5877      5877 26723

Use mice with Decision Tree to impute missing data.

imp.data <- mice(data, m=1, method='cart', printFlag=FALSE)
summary(imp.data)
## Multiply imputed data set
## Call:
## mice(data = data, m = 1, method = "cart", printFlag = FALSE)
## Number of multiple imputations:  1
## Missing cells per column:
##   GV_CURBWGT     GV_DVLAT    GV_DVLONG    GV_ENERGY     GV_LANES 
##           39         5877         5877         5877            3 
##   GV_MODELYR  GV_OTVEHWGT   GV_SPLIMIT   GV_WGTCDTR       OA_AGE 
##            0         1992          221            0           14 
##  OA_BAGDEPLY    OA_HEIGHT      OA_MAIS    OA_MANUSE       OA_SEX 
##            0         2116            0          385            0 
##    OA_WEIGHT      VE_GAD1  VE_ORIGAVTW  VE_WHEELBAS   VE_PDOF_TR 
##         2008            0          219            8         1864 
## GV_FOOTPRINT 
##          223 
## Imputation methods:
##   GV_CURBWGT     GV_DVLAT    GV_DVLONG    GV_ENERGY     GV_LANES 
##       "cart"       "cart"       "cart"       "cart"       "cart" 
##   GV_MODELYR  GV_OTVEHWGT   GV_SPLIMIT   GV_WGTCDTR       OA_AGE 
##       "cart"       "cart"       "cart"       "cart"       "cart" 
##  OA_BAGDEPLY    OA_HEIGHT      OA_MAIS    OA_MANUSE       OA_SEX 
##       "cart"       "cart"       "cart"       "cart"       "cart" 
##    OA_WEIGHT      VE_GAD1  VE_ORIGAVTW  VE_WHEELBAS   VE_PDOF_TR 
##       "cart"       "cart"       "cart"       "cart"       "cart" 
## GV_FOOTPRINT 
##       "cart" 
## VisitSequence:
##   GV_CURBWGT     GV_DVLAT    GV_DVLONG    GV_ENERGY     GV_LANES 
##            1            2            3            4            5 
##  GV_OTVEHWGT   GV_SPLIMIT       OA_AGE    OA_HEIGHT    OA_MANUSE 
##            7            8           10           12           14 
##    OA_WEIGHT  VE_ORIGAVTW  VE_WHEELBAS   VE_PDOF_TR GV_FOOTPRINT 
##           16           18           19           20           21 
## PredictorMatrix:
##              GV_CURBWGT GV_DVLAT GV_DVLONG GV_ENERGY GV_LANES GV_MODELYR
## GV_CURBWGT            0        1         1         1        1          1
## GV_DVLAT              1        0         1         1        1          1
## GV_DVLONG             1        1         0         1        1          1
## GV_ENERGY             1        1         1         0        1          1
## GV_LANES              1        1         1         1        0          1
## GV_MODELYR            0        0         0         0        0          0
## GV_OTVEHWGT           1        1         1         1        1          1
## GV_SPLIMIT            1        1         1         1        1          1
## GV_WGTCDTR            0        0         0         0        0          0
## OA_AGE                1        1         1         1        1          1
## OA_BAGDEPLY           0        0         0         0        0          0
## OA_HEIGHT             1        1         1         1        1          1
## OA_MAIS               0        0         0         0        0          0
## OA_MANUSE             1        1         1         1        1          1
## OA_SEX                0        0         0         0        0          0
## OA_WEIGHT             1        1         1         1        1          1
## VE_GAD1               0        0         0         0        0          0
## VE_ORIGAVTW           1        1         1         1        1          1
## VE_WHEELBAS           1        1         1         1        1          1
## VE_PDOF_TR            1        1         1         1        1          1
## GV_FOOTPRINT          1        1         1         1        1          1
##              GV_OTVEHWGT GV_SPLIMIT GV_WGTCDTR OA_AGE OA_BAGDEPLY
## GV_CURBWGT             1          1          1      1           1
## GV_DVLAT               1          1          1      1           1
## GV_DVLONG              1          1          1      1           1
## GV_ENERGY              1          1          1      1           1
## GV_LANES               1          1          1      1           1
## GV_MODELYR             0          0          0      0           0
## GV_OTVEHWGT            0          1          1      1           1
## GV_SPLIMIT             1          0          1      1           1
## GV_WGTCDTR             0          0          0      0           0
## OA_AGE                 1          1          1      0           1
## OA_BAGDEPLY            0          0          0      0           0
## OA_HEIGHT              1          1          1      1           1
## OA_MAIS                0          0          0      0           0
## OA_MANUSE              1          1          1      1           1
## OA_SEX                 0          0          0      0           0
## OA_WEIGHT              1          1          1      1           1
## VE_GAD1                0          0          0      0           0
## VE_ORIGAVTW            1          1          1      1           1
## VE_WHEELBAS            1          1          1      1           1
## VE_PDOF_TR             1          1          1      1           1
## GV_FOOTPRINT           1          1          1      1           1
##              OA_HEIGHT OA_MAIS OA_MANUSE OA_SEX OA_WEIGHT VE_GAD1
## GV_CURBWGT           1       1         1      1         1       1
## GV_DVLAT             1       1         1      1         1       1
## GV_DVLONG            1       1         1      1         1       1
## GV_ENERGY            1       1         1      1         1       1
## GV_LANES             1       1         1      1         1       1
## GV_MODELYR           0       0         0      0         0       0
## GV_OTVEHWGT          1       1         1      1         1       1
## GV_SPLIMIT           1       1         1      1         1       1
## GV_WGTCDTR           0       0         0      0         0       0
## OA_AGE               1       1         1      1         1       1
## OA_BAGDEPLY          0       0         0      0         0       0
## OA_HEIGHT            0       1         1      1         1       1
## OA_MAIS              0       0         0      0         0       0
## OA_MANUSE            1       1         0      1         1       1
## OA_SEX               0       0         0      0         0       0
## OA_WEIGHT            1       1         1      1         0       1
## VE_GAD1              0       0         0      0         0       0
## VE_ORIGAVTW          1       1         1      1         1       1
## VE_WHEELBAS          1       1         1      1         1       1
## VE_PDOF_TR           1       1         1      1         1       1
## GV_FOOTPRINT         1       1         1      1         1       1
##              VE_ORIGAVTW VE_WHEELBAS VE_PDOF_TR GV_FOOTPRINT
## GV_CURBWGT             1           1          1            1
## GV_DVLAT               1           1          1            1
## GV_DVLONG              1           1          1            1
## GV_ENERGY              1           1          1            1
## GV_LANES               1           1          1            1
## GV_MODELYR             0           0          0            0
## GV_OTVEHWGT            1           1          1            1
## GV_SPLIMIT             1           1          1            1
## GV_WGTCDTR             0           0          0            0
## OA_AGE                 1           1          1            1
## OA_BAGDEPLY            0           0          0            0
## OA_HEIGHT              1           1          1            1
## OA_MAIS                0           0          0            0
## OA_MANUSE              1           1          1            1
## OA_SEX                 0           0          0            0
## OA_WEIGHT              1           1          1            1
## VE_GAD1                0           0          0            0
## VE_ORIGAVTW            0           1          1            1
## VE_WHEELBAS            1           0          1            1
## VE_PDOF_TR             1           1          0            1
## GV_FOOTPRINT           1           1          1            0
## Random generator seed value:  NA

Write imputted mean values from decision tree model.

# write results
write.mice.imputation(mi.res=imp.data, name="mice_imp_cart")
## 2018-03-15 22:01:30 
## 
##  /Users/davidleonardi/Projects/KE5107_BayesianNetworks/mice_imp_cart 
## 
## Multiply imputed data set
## Call:
## mice(data = data, m = 1, method = "cart", printFlag = FALSE)
## Number of multiple imputations:  1
## Missing cells per column:
##   GV_CURBWGT     GV_DVLAT    GV_DVLONG    GV_ENERGY     GV_LANES 
##           39         5877         5877         5877            3 
##   GV_MODELYR  GV_OTVEHWGT   GV_SPLIMIT   GV_WGTCDTR       OA_AGE 
##            0         1992          221            0           14 
##  OA_BAGDEPLY    OA_HEIGHT      OA_MAIS    OA_MANUSE       OA_SEX 
##            0         2116            0          385            0 
##    OA_WEIGHT      VE_GAD1  VE_ORIGAVTW  VE_WHEELBAS   VE_PDOF_TR 
##         2008            0          219            8         1864 
## GV_FOOTPRINT 
##          223 
## Imputation methods:
##   GV_CURBWGT     GV_DVLAT    GV_DVLONG    GV_ENERGY     GV_LANES 
##       "cart"       "cart"       "cart"       "cart"       "cart" 
##   GV_MODELYR  GV_OTVEHWGT   GV_SPLIMIT   GV_WGTCDTR       OA_AGE 
##       "cart"       "cart"       "cart"       "cart"       "cart" 
##  OA_BAGDEPLY    OA_HEIGHT      OA_MAIS    OA_MANUSE       OA_SEX 
##       "cart"       "cart"       "cart"       "cart"       "cart" 
##    OA_WEIGHT      VE_GAD1  VE_ORIGAVTW  VE_WHEELBAS   VE_PDOF_TR 
##       "cart"       "cart"       "cart"       "cart"       "cart" 
## GV_FOOTPRINT 
##       "cart" 
## VisitSequence:
##   GV_CURBWGT     GV_DVLAT    GV_DVLONG    GV_ENERGY     GV_LANES 
##            1            2            3            4            5 
##  GV_OTVEHWGT   GV_SPLIMIT       OA_AGE    OA_HEIGHT    OA_MANUSE 
##            7            8           10           12           14 
##    OA_WEIGHT  VE_ORIGAVTW  VE_WHEELBAS   VE_PDOF_TR GV_FOOTPRINT 
##           16           18           19           20           21 
## PredictorMatrix:
##              GV_CURBWGT GV_DVLAT GV_DVLONG GV_ENERGY GV_LANES GV_MODELYR
## GV_CURBWGT            0        1         1         1        1          1
## GV_DVLAT              1        0         1         1        1          1
## GV_DVLONG             1        1         0         1        1          1
## GV_ENERGY             1        1         1         0        1          1
## GV_LANES              1        1         1         1        0          1
## GV_MODELYR            0        0         0         0        0          0
## GV_OTVEHWGT           1        1         1         1        1          1
## GV_SPLIMIT            1        1         1         1        1          1
## GV_WGTCDTR            0        0         0         0        0          0
## OA_AGE                1        1         1         1        1          1
## OA_BAGDEPLY           0        0         0         0        0          0
## OA_HEIGHT             1        1         1         1        1          1
## OA_MAIS               0        0         0         0        0          0
## OA_MANUSE             1        1         1         1        1          1
## OA_SEX                0        0         0         0        0          0
## OA_WEIGHT             1        1         1         1        1          1
## VE_GAD1               0        0         0         0        0          0
## VE_ORIGAVTW           1        1         1         1        1          1
## VE_WHEELBAS           1        1         1         1        1          1
## VE_PDOF_TR            1        1         1         1        1          1
## GV_FOOTPRINT          1        1         1         1        1          1
##              GV_OTVEHWGT GV_SPLIMIT GV_WGTCDTR OA_AGE OA_BAGDEPLY
## GV_CURBWGT             1          1          1      1           1
## GV_DVLAT               1          1          1      1           1
## GV_DVLONG              1          1          1      1           1
## GV_ENERGY              1          1          1      1           1
## GV_LANES               1          1          1      1           1
## GV_MODELYR             0          0          0      0           0
## GV_OTVEHWGT            0          1          1      1           1
## GV_SPLIMIT             1          0          1      1           1
## GV_WGTCDTR             0          0          0      0           0
## OA_AGE                 1          1          1      0           1
## OA_BAGDEPLY            0          0          0      0           0
## OA_HEIGHT              1          1          1      1           1
## OA_MAIS                0          0          0      0           0
## OA_MANUSE              1          1          1      1           1
## OA_SEX                 0          0          0      0           0
## OA_WEIGHT              1          1          1      1           1
## VE_GAD1                0          0          0      0           0
## VE_ORIGAVTW            1          1          1      1           1
## VE_WHEELBAS            1          1          1      1           1
## VE_PDOF_TR             1          1          1      1           1
## GV_FOOTPRINT           1          1          1      1           1
##              OA_HEIGHT OA_MAIS OA_MANUSE OA_SEX OA_WEIGHT VE_GAD1
## GV_CURBWGT           1       1         1      1         1       1
## GV_DVLAT             1       1         1      1         1       1
## GV_DVLONG            1       1         1      1         1       1
## GV_ENERGY            1       1         1      1         1       1
## GV_LANES             1       1         1      1         1       1
## GV_MODELYR           0       0         0      0         0       0
## GV_OTVEHWGT          1       1         1      1         1       1
## GV_SPLIMIT           1       1         1      1         1       1
## GV_WGTCDTR           0       0         0      0         0       0
## OA_AGE               1       1         1      1         1       1
## OA_BAGDEPLY          0       0         0      0         0       0
## OA_HEIGHT            0       1         1      1         1       1
## OA_MAIS              0       0         0      0         0       0
## OA_MANUSE            1       1         0      1         1       1
## OA_SEX               0       0         0      0         0       0
## OA_WEIGHT            1       1         1      1         0       1
## VE_GAD1              0       0         0      0         0       0
## VE_ORIGAVTW          1       1         1      1         1       1
## VE_WHEELBAS          1       1         1      1         1       1
## VE_PDOF_TR           1       1         1      1         1       1
## GV_FOOTPRINT         1       1         1      1         1       1
##              VE_ORIGAVTW VE_WHEELBAS VE_PDOF_TR GV_FOOTPRINT
## GV_CURBWGT             1           1          1            1
## GV_DVLAT               1           1          1            1
## GV_DVLONG              1           1          1            1
## GV_ENERGY              1           1          1            1
## GV_LANES               1           1          1            1
## GV_MODELYR             0           0          0            0
## GV_OTVEHWGT            1           1          1            1
## GV_SPLIMIT             1           1          1            1
## GV_WGTCDTR             0           0          0            0
## OA_AGE                 1           1          1            1
## OA_BAGDEPLY            0           0          0            0
## OA_HEIGHT              1           1          1            1
## OA_MAIS                0           0          0            0
## OA_MANUSE              1           1          1            1
## OA_SEX                 0           0          0            0
## OA_WEIGHT              1           1          1            1
## VE_GAD1                0           0          0            0
## VE_ORIGAVTW            0           1          1            1
## VE_WHEELBAS            1           0          1            1
## VE_PDOF_TR             1           1          0            1
## GV_FOOTPRINT           1           1          1            0
## Random generator seed value:  NA 
## NULL
## 
## 
## 
## To cite R in publications use:
## 
##   R Core Team (2017). R: A language and environment for
##   statistical computing. R Foundation for Statistical Computing,
##   Vienna, Austria. URL https://www.R-project.org/.
## 
## A BibTeX entry for LaTeX users is
## 
##   @Manual{,
##     title = {R: A Language and Environment for Statistical Computing},
##     author = {{R Core Team}},
##     organization = {R Foundation for Statistical Computing},
##     address = {Vienna, Austria},
##     year = {2017},
##     url = {https://www.R-project.org/},
##   }
## 
## We have invested a lot of time and effort in creating R, please
## cite it when using it for data analysis. See also
## 'citation("pkgname")' for citing R packages.
## 
## 
## To cite mice in publications use:
## 
##   Stef van Buuren, Karin Groothuis-Oudshoorn (2011). mice:
##   Multivariate Imputation by Chained Equations in R. Journal of
##   Statistical Software, 45(3), 1-67. URL
##   http://www.jstatsoft.org/v45/i03/.
## 
## A BibTeX entry for LaTeX users is
## 
##   @Article{,
##     title = {{mice}: Multivariate Imputation by Chained Equations in R},
##     author = {Stef {van Buuren} and Karin Groothuis-Oudshoorn},
##     journal = {Journal of Statistical Software},
##     year = {2011},
##     volume = {45},
##     number = {3},
##     pages = {1--67},
##     url = {http://www.jstatsoft.org/v45/i03/},
##   }
## 
##                                                                                           sysname 
##                                                                                          "Darwin" 
##                                                                                           release 
##                                                                                          "16.7.0" 
##                                                                                           version 
## "Darwin Kernel Version 16.7.0: Thu Jan 11 22:59:40 PST 2018; root:xnu-3789.73.8~1/RELEASE_X86_64" 
##                                                                                          nodename 
##                                                                    "Chatarinas-MacBook-Pro.local" 
##                                                                                           machine 
##                                                                                          "x86_64" 
##                                                                                             login 
##                                                                                   "davidleonardi" 
##                                                                                              user 
##                                                                                   "davidleonardi" 
##                                                                                    effective_user 
##                                                                                   "davidleonardi" 
## R version 3.4.3 (2017-11-30)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Sierra 10.12.6
## 
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] C
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] ggplot2_2.2.1   miceadds_2.9-15 mice_2.46.0     lattice_0.20-35
## [5] Amelia_1.7.4    Rcpp_0.12.15   
## 
## loaded via a namespace (and not attached):
##  [1] lavaan_0.5-23.1097    mitools_2.3           splines_3.4.3        
##  [4] colorspace_1.3-2      htmltools_0.3.6       stats4_3.4.3         
##  [7] yaml_2.1.17           mgcv_1.8-22           rlang_0.2.0          
## [10] survival_2.41-3       pillar_1.2.1          nloptr_1.0.4         
## [13] foreign_0.8-69        lavaan.survey_1.1.3.1 plyr_1.8.4           
## [16] mirt_1.26.3           GPArotation_2014.11-1 stringr_1.3.0        
## [19] munsell_0.4.3         CDM_6.1-10            gtable_0.2.0         
## [22] mvtnorm_1.0-7         coda_0.19-1           evaluate_0.10.1      
## [25] knitr_1.20            permute_0.9-4         sirt_2.5-45          
## [28] parallel_3.4.3        backports_1.1.2       scales_0.5.0         
## [31] vegan_2.4-6           lme4_1.1-15           polycor_0.7-9        
## [34] mnormt_1.5-5          digest_0.6.15         stringi_1.1.6        
## [37] survey_3.33-2         grid_3.4.3            rprojroot_1.3-2      
## [40] quadprog_1.5-5        tools_3.4.3           magrittr_1.5         
## [43] lazyeval_0.2.1        tibble_1.4.2          cluster_2.0.6        
## [46] pbivnorm_0.6.0        TAM_2.9-35            MASS_7.3-47          
## [49] Matrix_1.2-12         minqa_1.2.4           rmarkdown_1.9        
## [52] rpart_4.1-11          sfsmisc_1.1-2         nnet_7.3-12          
## [55] nlme_3.1-131          compiler_3.4.3       
## 
##  1
## Data values written to /Users/davidleonardi/Projects/KE5107_BayesianNetworks/mice_imp_cart/mice_imp_cart__SPSS.txt 
## Syntax file written to /Users/davidleonardi/Projects/KE5107_BayesianNetworks/mice_imp_cart/mice_imp_cart__SPSS.sps

Compare it with Mean value.

imp.data_raw_mean <- mice(data, m=1, defaultMethod=c('mean', 'cart', 'cart', 'cart'), printFlag=FALSE)
summary(imp.data_raw_mean)
## Multiply imputed data set
## Call:
## mice(data = data, m = 1, defaultMethod = c("mean", "cart", "cart", 
##     "cart"), printFlag = FALSE)
## Number of multiple imputations:  1
## Missing cells per column:
##   GV_CURBWGT     GV_DVLAT    GV_DVLONG    GV_ENERGY     GV_LANES 
##           39         5877         5877         5877            3 
##   GV_MODELYR  GV_OTVEHWGT   GV_SPLIMIT   GV_WGTCDTR       OA_AGE 
##            0         1992          221            0           14 
##  OA_BAGDEPLY    OA_HEIGHT      OA_MAIS    OA_MANUSE       OA_SEX 
##            0         2116            0          385            0 
##    OA_WEIGHT      VE_GAD1  VE_ORIGAVTW  VE_WHEELBAS   VE_PDOF_TR 
##         2008            0          219            8         1864 
## GV_FOOTPRINT 
##          223 
## Imputation methods:
##   GV_CURBWGT     GV_DVLAT    GV_DVLONG    GV_ENERGY     GV_LANES 
##       "mean"       "mean"       "mean"       "mean"       "cart" 
##   GV_MODELYR  GV_OTVEHWGT   GV_SPLIMIT   GV_WGTCDTR       OA_AGE 
##           ""       "mean"       "mean"           ""       "mean" 
##  OA_BAGDEPLY    OA_HEIGHT      OA_MAIS    OA_MANUSE       OA_SEX 
##           ""       "mean"           ""       "cart"           "" 
##    OA_WEIGHT      VE_GAD1  VE_ORIGAVTW  VE_WHEELBAS   VE_PDOF_TR 
##       "mean"           ""       "mean"       "mean"       "mean" 
## GV_FOOTPRINT 
##       "mean" 
## VisitSequence:
##   GV_CURBWGT     GV_DVLAT    GV_DVLONG    GV_ENERGY     GV_LANES 
##            1            2            3            4            5 
##  GV_OTVEHWGT   GV_SPLIMIT       OA_AGE    OA_HEIGHT    OA_MANUSE 
##            7            8           10           12           14 
##    OA_WEIGHT  VE_ORIGAVTW  VE_WHEELBAS   VE_PDOF_TR GV_FOOTPRINT 
##           16           18           19           20           21 
## PredictorMatrix:
##              GV_CURBWGT GV_DVLAT GV_DVLONG GV_ENERGY GV_LANES GV_MODELYR
## GV_CURBWGT            0        1         1         1        1          1
## GV_DVLAT              1        0         1         1        1          1
## GV_DVLONG             1        1         0         1        1          1
## GV_ENERGY             1        1         1         0        1          1
## GV_LANES              1        1         1         1        0          1
## GV_MODELYR            0        0         0         0        0          0
## GV_OTVEHWGT           1        1         1         1        1          1
## GV_SPLIMIT            1        1         1         1        1          1
## GV_WGTCDTR            0        0         0         0        0          0
## OA_AGE                1        1         1         1        1          1
## OA_BAGDEPLY           0        0         0         0        0          0
## OA_HEIGHT             1        1         1         1        1          1
## OA_MAIS               0        0         0         0        0          0
## OA_MANUSE             1        1         1         1        1          1
## OA_SEX                0        0         0         0        0          0
## OA_WEIGHT             1        1         1         1        1          1
## VE_GAD1               0        0         0         0        0          0
## VE_ORIGAVTW           1        1         1         1        1          1
## VE_WHEELBAS           1        1         1         1        1          1
## VE_PDOF_TR            1        1         1         1        1          1
## GV_FOOTPRINT          1        1         1         1        1          1
##              GV_OTVEHWGT GV_SPLIMIT GV_WGTCDTR OA_AGE OA_BAGDEPLY
## GV_CURBWGT             1          1          1      1           1
## GV_DVLAT               1          1          1      1           1
## GV_DVLONG              1          1          1      1           1
## GV_ENERGY              1          1          1      1           1
## GV_LANES               1          1          1      1           1
## GV_MODELYR             0          0          0      0           0
## GV_OTVEHWGT            0          1          1      1           1
## GV_SPLIMIT             1          0          1      1           1
## GV_WGTCDTR             0          0          0      0           0
## OA_AGE                 1          1          1      0           1
## OA_BAGDEPLY            0          0          0      0           0
## OA_HEIGHT              1          1          1      1           1
## OA_MAIS                0          0          0      0           0
## OA_MANUSE              1          1          1      1           1
## OA_SEX                 0          0          0      0           0
## OA_WEIGHT              1          1          1      1           1
## VE_GAD1                0          0          0      0           0
## VE_ORIGAVTW            1          1          1      1           1
## VE_WHEELBAS            1          1          1      1           1
## VE_PDOF_TR             1          1          1      1           1
## GV_FOOTPRINT           1          1          1      1           1
##              OA_HEIGHT OA_MAIS OA_MANUSE OA_SEX OA_WEIGHT VE_GAD1
## GV_CURBWGT           1       1         1      1         1       1
## GV_DVLAT             1       1         1      1         1       1
## GV_DVLONG            1       1         1      1         1       1
## GV_ENERGY            1       1         1      1         1       1
## GV_LANES             1       1         1      1         1       1
## GV_MODELYR           0       0         0      0         0       0
## GV_OTVEHWGT          1       1         1      1         1       1
## GV_SPLIMIT           1       1         1      1         1       1
## GV_WGTCDTR           0       0         0      0         0       0
## OA_AGE               1       1         1      1         1       1
## OA_BAGDEPLY          0       0         0      0         0       0
## OA_HEIGHT            0       1         1      1         1       1
## OA_MAIS              0       0         0      0         0       0
## OA_MANUSE            1       1         0      1         1       1
## OA_SEX               0       0         0      0         0       0
## OA_WEIGHT            1       1         1      1         0       1
## VE_GAD1              0       0         0      0         0       0
## VE_ORIGAVTW          1       1         1      1         1       1
## VE_WHEELBAS          1       1         1      1         1       1
## VE_PDOF_TR           1       1         1      1         1       1
## GV_FOOTPRINT         1       1         1      1         1       1
##              VE_ORIGAVTW VE_WHEELBAS VE_PDOF_TR GV_FOOTPRINT
## GV_CURBWGT             1           1          1            1
## GV_DVLAT               1           1          1            1
## GV_DVLONG              1           1          1            1
## GV_ENERGY              1           1          1            1
## GV_LANES               1           1          1            1
## GV_MODELYR             0           0          0            0
## GV_OTVEHWGT            1           1          1            1
## GV_SPLIMIT             1           1          1            1
## GV_WGTCDTR             0           0          0            0
## OA_AGE                 1           1          1            1
## OA_BAGDEPLY            0           0          0            0
## OA_HEIGHT              1           1          1            1
## OA_MAIS                0           0          0            0
## OA_MANUSE              1           1          1            1
## OA_SEX                 0           0          0            0
## OA_WEIGHT              1           1          1            1
## VE_GAD1                0           0          0            0
## VE_ORIGAVTW            0           1          1            1
## VE_WHEELBAS            1           0          1            1
## VE_PDOF_TR             1           1          0            1
## GV_FOOTPRINT           1           1          1            0
## Random generator seed value:  NA

Write imputted mean values from mean model.

# write results
write.mice.imputation(mi.res=imp.data_raw_mean, name="mice_imp_mean" )
## 2018-03-15 22:02:44 
## 
##  /Users/davidleonardi/Projects/KE5107_BayesianNetworks/mice_imp_mean 
## 
## Multiply imputed data set
## Call:
## mice(data = data, m = 1, defaultMethod = c("mean", "cart", "cart", 
##     "cart"), printFlag = FALSE)
## Number of multiple imputations:  1
## Missing cells per column:
##   GV_CURBWGT     GV_DVLAT    GV_DVLONG    GV_ENERGY     GV_LANES 
##           39         5877         5877         5877            3 
##   GV_MODELYR  GV_OTVEHWGT   GV_SPLIMIT   GV_WGTCDTR       OA_AGE 
##            0         1992          221            0           14 
##  OA_BAGDEPLY    OA_HEIGHT      OA_MAIS    OA_MANUSE       OA_SEX 
##            0         2116            0          385            0 
##    OA_WEIGHT      VE_GAD1  VE_ORIGAVTW  VE_WHEELBAS   VE_PDOF_TR 
##         2008            0          219            8         1864 
## GV_FOOTPRINT 
##          223 
## Imputation methods:
##   GV_CURBWGT     GV_DVLAT    GV_DVLONG    GV_ENERGY     GV_LANES 
##       "mean"       "mean"       "mean"       "mean"       "cart" 
##   GV_MODELYR  GV_OTVEHWGT   GV_SPLIMIT   GV_WGTCDTR       OA_AGE 
##           ""       "mean"       "mean"           ""       "mean" 
##  OA_BAGDEPLY    OA_HEIGHT      OA_MAIS    OA_MANUSE       OA_SEX 
##           ""       "mean"           ""       "cart"           "" 
##    OA_WEIGHT      VE_GAD1  VE_ORIGAVTW  VE_WHEELBAS   VE_PDOF_TR 
##       "mean"           ""       "mean"       "mean"       "mean" 
## GV_FOOTPRINT 
##       "mean" 
## VisitSequence:
##   GV_CURBWGT     GV_DVLAT    GV_DVLONG    GV_ENERGY     GV_LANES 
##            1            2            3            4            5 
##  GV_OTVEHWGT   GV_SPLIMIT       OA_AGE    OA_HEIGHT    OA_MANUSE 
##            7            8           10           12           14 
##    OA_WEIGHT  VE_ORIGAVTW  VE_WHEELBAS   VE_PDOF_TR GV_FOOTPRINT 
##           16           18           19           20           21 
## PredictorMatrix:
##              GV_CURBWGT GV_DVLAT GV_DVLONG GV_ENERGY GV_LANES GV_MODELYR
## GV_CURBWGT            0        1         1         1        1          1
## GV_DVLAT              1        0         1         1        1          1
## GV_DVLONG             1        1         0         1        1          1
## GV_ENERGY             1        1         1         0        1          1
## GV_LANES              1        1         1         1        0          1
## GV_MODELYR            0        0         0         0        0          0
## GV_OTVEHWGT           1        1         1         1        1          1
## GV_SPLIMIT            1        1         1         1        1          1
## GV_WGTCDTR            0        0         0         0        0          0
## OA_AGE                1        1         1         1        1          1
## OA_BAGDEPLY           0        0         0         0        0          0
## OA_HEIGHT             1        1         1         1        1          1
## OA_MAIS               0        0         0         0        0          0
## OA_MANUSE             1        1         1         1        1          1
## OA_SEX                0        0         0         0        0          0
## OA_WEIGHT             1        1         1         1        1          1
## VE_GAD1               0        0         0         0        0          0
## VE_ORIGAVTW           1        1         1         1        1          1
## VE_WHEELBAS           1        1         1         1        1          1
## VE_PDOF_TR            1        1         1         1        1          1
## GV_FOOTPRINT          1        1         1         1        1          1
##              GV_OTVEHWGT GV_SPLIMIT GV_WGTCDTR OA_AGE OA_BAGDEPLY
## GV_CURBWGT             1          1          1      1           1
## GV_DVLAT               1          1          1      1           1
## GV_DVLONG              1          1          1      1           1
## GV_ENERGY              1          1          1      1           1
## GV_LANES               1          1          1      1           1
## GV_MODELYR             0          0          0      0           0
## GV_OTVEHWGT            0          1          1      1           1
## GV_SPLIMIT             1          0          1      1           1
## GV_WGTCDTR             0          0          0      0           0
## OA_AGE                 1          1          1      0           1
## OA_BAGDEPLY            0          0          0      0           0
## OA_HEIGHT              1          1          1      1           1
## OA_MAIS                0          0          0      0           0
## OA_MANUSE              1          1          1      1           1
## OA_SEX                 0          0          0      0           0
## OA_WEIGHT              1          1          1      1           1
## VE_GAD1                0          0          0      0           0
## VE_ORIGAVTW            1          1          1      1           1
## VE_WHEELBAS            1          1          1      1           1
## VE_PDOF_TR             1          1          1      1           1
## GV_FOOTPRINT           1          1          1      1           1
##              OA_HEIGHT OA_MAIS OA_MANUSE OA_SEX OA_WEIGHT VE_GAD1
## GV_CURBWGT           1       1         1      1         1       1
## GV_DVLAT             1       1         1      1         1       1
## GV_DVLONG            1       1         1      1         1       1
## GV_ENERGY            1       1         1      1         1       1
## GV_LANES             1       1         1      1         1       1
## GV_MODELYR           0       0         0      0         0       0
## GV_OTVEHWGT          1       1         1      1         1       1
## GV_SPLIMIT           1       1         1      1         1       1
## GV_WGTCDTR           0       0         0      0         0       0
## OA_AGE               1       1         1      1         1       1
## OA_BAGDEPLY          0       0         0      0         0       0
## OA_HEIGHT            0       1         1      1         1       1
## OA_MAIS              0       0         0      0         0       0
## OA_MANUSE            1       1         0      1         1       1
## OA_SEX               0       0         0      0         0       0
## OA_WEIGHT            1       1         1      1         0       1
## VE_GAD1              0       0         0      0         0       0
## VE_ORIGAVTW          1       1         1      1         1       1
## VE_WHEELBAS          1       1         1      1         1       1
## VE_PDOF_TR           1       1         1      1         1       1
## GV_FOOTPRINT         1       1         1      1         1       1
##              VE_ORIGAVTW VE_WHEELBAS VE_PDOF_TR GV_FOOTPRINT
## GV_CURBWGT             1           1          1            1
## GV_DVLAT               1           1          1            1
## GV_DVLONG              1           1          1            1
## GV_ENERGY              1           1          1            1
## GV_LANES               1           1          1            1
## GV_MODELYR             0           0          0            0
## GV_OTVEHWGT            1           1          1            1
## GV_SPLIMIT             1           1          1            1
## GV_WGTCDTR             0           0          0            0
## OA_AGE                 1           1          1            1
## OA_BAGDEPLY            0           0          0            0
## OA_HEIGHT              1           1          1            1
## OA_MAIS                0           0          0            0
## OA_MANUSE              1           1          1            1
## OA_SEX                 0           0          0            0
## OA_WEIGHT              1           1          1            1
## VE_GAD1                0           0          0            0
## VE_ORIGAVTW            0           1          1            1
## VE_WHEELBAS            1           0          1            1
## VE_PDOF_TR             1           1          0            1
## GV_FOOTPRINT           1           1          1            0
## Random generator seed value:  NA 
## NULL
## 
## 
## 
## To cite R in publications use:
## 
##   R Core Team (2017). R: A language and environment for
##   statistical computing. R Foundation for Statistical Computing,
##   Vienna, Austria. URL https://www.R-project.org/.
## 
## A BibTeX entry for LaTeX users is
## 
##   @Manual{,
##     title = {R: A Language and Environment for Statistical Computing},
##     author = {{R Core Team}},
##     organization = {R Foundation for Statistical Computing},
##     address = {Vienna, Austria},
##     year = {2017},
##     url = {https://www.R-project.org/},
##   }
## 
## We have invested a lot of time and effort in creating R, please
## cite it when using it for data analysis. See also
## 'citation("pkgname")' for citing R packages.
## 
## 
## To cite mice in publications use:
## 
##   Stef van Buuren, Karin Groothuis-Oudshoorn (2011). mice:
##   Multivariate Imputation by Chained Equations in R. Journal of
##   Statistical Software, 45(3), 1-67. URL
##   http://www.jstatsoft.org/v45/i03/.
## 
## A BibTeX entry for LaTeX users is
## 
##   @Article{,
##     title = {{mice}: Multivariate Imputation by Chained Equations in R},
##     author = {Stef {van Buuren} and Karin Groothuis-Oudshoorn},
##     journal = {Journal of Statistical Software},
##     year = {2011},
##     volume = {45},
##     number = {3},
##     pages = {1--67},
##     url = {http://www.jstatsoft.org/v45/i03/},
##   }
## 
##                                                                                           sysname 
##                                                                                          "Darwin" 
##                                                                                           release 
##                                                                                          "16.7.0" 
##                                                                                           version 
## "Darwin Kernel Version 16.7.0: Thu Jan 11 22:59:40 PST 2018; root:xnu-3789.73.8~1/RELEASE_X86_64" 
##                                                                                          nodename 
##                                                                    "Chatarinas-MacBook-Pro.local" 
##                                                                                           machine 
##                                                                                          "x86_64" 
##                                                                                             login 
##                                                                                   "davidleonardi" 
##                                                                                              user 
##                                                                                   "davidleonardi" 
##                                                                                    effective_user 
##                                                                                   "davidleonardi" 
## R version 3.4.3 (2017-11-30)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Sierra 10.12.6
## 
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] C
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] ggplot2_2.2.1   miceadds_2.9-15 mice_2.46.0     lattice_0.20-35
## [5] Amelia_1.7.4    Rcpp_0.12.15   
## 
## loaded via a namespace (and not attached):
##  [1] lavaan_0.5-23.1097    mitools_2.3           splines_3.4.3        
##  [4] colorspace_1.3-2      htmltools_0.3.6       stats4_3.4.3         
##  [7] yaml_2.1.17           mgcv_1.8-22           rlang_0.2.0          
## [10] survival_2.41-3       pillar_1.2.1          nloptr_1.0.4         
## [13] foreign_0.8-69        lavaan.survey_1.1.3.1 plyr_1.8.4           
## [16] mirt_1.26.3           GPArotation_2014.11-1 stringr_1.3.0        
## [19] munsell_0.4.3         CDM_6.1-10            gtable_0.2.0         
## [22] mvtnorm_1.0-7         coda_0.19-1           evaluate_0.10.1      
## [25] knitr_1.20            permute_0.9-4         sirt_2.5-45          
## [28] parallel_3.4.3        backports_1.1.2       scales_0.5.0         
## [31] vegan_2.4-6           lme4_1.1-15           polycor_0.7-9        
## [34] mnormt_1.5-5          digest_0.6.15         stringi_1.1.6        
## [37] survey_3.33-2         grid_3.4.3            rprojroot_1.3-2      
## [40] quadprog_1.5-5        tools_3.4.3           magrittr_1.5         
## [43] lazyeval_0.2.1        tibble_1.4.2          cluster_2.0.6        
## [46] pbivnorm_0.6.0        TAM_2.9-35            MASS_7.3-47          
## [49] Matrix_1.2-12         minqa_1.2.4           rmarkdown_1.9        
## [52] rpart_4.1-11          sfsmisc_1.1-2         nnet_7.3-12          
## [55] nlme_3.1-131          compiler_3.4.3       
## 
##  1
## Data values written to /Users/davidleonardi/Projects/KE5107_BayesianNetworks/mice_imp_mean/mice_imp_mean__SPSS.txt 
## Syntax file written to /Users/davidleonardi/Projects/KE5107_BayesianNetworks/mice_imp_mean/mice_imp_mean__SPSS.sps

Plot GV_DVLAT and VE_PDOF_TR for imputed data using Decision Tree.

xyplot(imp.data, GV_DVLAT ~ VE_PDOF_TR)

Plot GV_DVLONG and VE_PDOF_TR for imputed data using Decision Tree.

xyplot(imp.data, GV_DVLONG ~ VE_PDOF_TR)

Plot GV_DVLAT and GV_FOOTPRINT for imputed data using Decision Tree.

xyplot(imp.data, GV_DVLAT ~ GV_FOOTPRINT)

Plot GV_DVLAT and GV_FOOTPRINT for imputed data using Decision Tree.

xyplot(imp.data, GV_DVLONG ~ GV_FOOTPRINT)

Plot GV_DVLAT and VE_PDOF_TR for imputed data using Mean value.

xyplot(imp.data_raw_mean, GV_DVLAT ~ VE_PDOF_TR)

Plot GV_DVLONG and VE_PDOF_TR for imputed data using Mean value.

xyplot(imp.data_raw_mean, GV_DVLONG ~ VE_PDOF_TR)

Plot GV_DVLAT and GV_FOOTPRINT for imputed data using Mean value.

xyplot(imp.data_raw_mean, GV_DVLAT ~ GV_FOOTPRINT)

Plot GV_DVLONG and GV_FOOTPRINT for imputed data using Mean value.

xyplot(imp.data_raw_mean, GV_DVLONG ~ GV_FOOTPRINT)

Save the imputed data.

data_complete <- complete(imp.data)
write.csv(data_complete, "./vehicle_safety_imputed_data.csv")